The way I see it is that Boeing designed the 737 and wrote the book based on exhaustive testing by their very experienced test pilots. Boeing generally don't put in a "not recommended" into the FCTM without very good reason. If the auto-throttle is MEL inoperative you can still operate the aircraft which in turn means it is safe to fly with the autothrottle turned off.. Best advice I can offer is to stick to the Boeing recommendation.